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- PDB-5eib: Crystal structure of CPAP PN2-3 C-terminal loop-helix in complex ... -

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Basic information

Entry
Database: PDB / ID: 5eib
TitleCrystal structure of CPAP PN2-3 C-terminal loop-helix in complex with DARPin-tubulin
Components
  • Designed ankyrin repeat proteinDARPin
  • Peptide from Centromere protein J
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / PN2-3 / Tubulin complex
Function / homology
Function and homology information


astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / positive regulation of non-motile cilium assembly / positive regulation of centriole replication / motile cilium assembly ...astral microtubule nucleation / centriole elongation / gamma-tubulin small complex / positive regulation of centriole elongation / positive regulation of establishment of protein localization / regulation of centriole replication / procentriole replication complex / positive regulation of non-motile cilium assembly / positive regulation of centriole replication / motile cilium assembly / positive regulation of spindle assembly / microtubule nucleation / non-motile cilium assembly / gamma-tubulin binding / positive regulation of axon guidance / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / smoothened signaling pathway / microtubule polymerization / centriole replication / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / cytoplasmic microtubule / microtubule-based process / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / cellular response to interleukin-4 / centriole / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of receptor signaling pathway via JAK-STAT / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-stranded RNA binding / mitotic cell cycle / nervous system development / microtubule / transcription coactivator activity / protein heterodimerization activity / cell division / protein domain specific binding / GTPase activity / centrosome / ubiquitin protein ligase binding / GTP binding / protein kinase binding / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
T-complex protein 10, C-terminal domain / T-complex protein 10 family / T-complex protein 10 C-terminus / : / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. ...T-complex protein 10, C-terminal domain / T-complex protein 10 family / T-complex protein 10 C-terminus / : / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1B chain / Tubulin beta-2B chain / Centromere protein J
Similarity search - Component
Biological speciessynthetic construct (others)
Bos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLi, H. / Zheng, X.
CitationJournal: Nat Commun / Year: 2016
Title: Molecular basis for CPAP-tubulin interaction in controlling centriolar and ciliary length
Authors: Zheng, X. / Ramani, A. / Soni, K. / Gottardo, M. / Zheng, S. / Ming Gooi, L. / Li, W. / Feng, S. / Mariappan, A. / Wason, A. / Widlund, P. / Pozniakovsky, A. / Poser, I. / Deng, H. / Ou, G. ...Authors: Zheng, X. / Ramani, A. / Soni, K. / Gottardo, M. / Zheng, S. / Ming Gooi, L. / Li, W. / Feng, S. / Mariappan, A. / Wason, A. / Widlund, P. / Pozniakovsky, A. / Poser, I. / Deng, H. / Ou, G. / Riparbelli, M. / Giuliano, C. / Hyman, A.A. / Sattler, M. / Gopalakrishnan, J. / Li, H.
History
DepositionOct 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Designed ankyrin repeat protein
F: Peptide from Centromere protein J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,9698
Polymers120,8744
Non-polymers1,0954
Water10,755597
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-55 kcal/mol
Surface area37200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.856, 91.116, 83.310
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules CDE

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49983.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856
#3: Protein Designed ankyrin repeat protein / DARPin


Mass: 17998.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Protein/peptide , 1 types, 1 molecules F

#4: Protein/peptide Peptide from Centromere protein J / / CENP-J / Centrosomal P4.1-associated protein / LAG-3-associated protein / LYST-interacting protein 1


Mass: 2687.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HC77

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Non-polymers , 3 types, 601 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUE C201S IS BASED ON REFERENCE 1 OF DATABASE Q6B856 (TBB2B_BOVIN).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: potassium sodium tartrate, PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2015 / Details: ADSC Quantum 315r
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 63572 / % possible obs: 99.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.128 / Χ2: 1.653 / Net I/av σ(I): 16.8 / Net I/σ(I): 8.1 / Num. measured all: 291375
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.144.60.89931391.36798.2
2.14-2.184.60.83331351.39298
2.18-2.224.60.75131051.39998.3
2.22-2.264.50.61831441.46698.4
2.26-2.314.60.61231741.38998.7
2.31-2.374.60.51331151.39198.5
2.37-2.424.60.44231501.36998.6
2.42-2.494.60.38731521.39599.3
2.49-2.564.60.33531951.39899.3
2.56-2.654.60.29131531.54799.4
2.65-2.744.60.25632171.59699.3
2.74-2.854.60.21431791.6899.6
2.85-2.984.60.17431811.75699.6
2.98-3.144.60.13831881.86399.8
3.14-3.334.60.10832271.98399.8
3.33-3.594.60.08131761.87999.6
3.59-3.954.40.0631971.86298.9
3.95-4.524.70.0532191.926100
4.52-5.74.70.04632392.21899.9
5.7-504.60.0432872.08899.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DRX

4drx


Resolution: 2.1→41.347 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 3127 4.92 %
Rwork0.1776 --
obs0.1797 63538 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→41.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8016 0 66 597 8679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018257
X-RAY DIFFRACTIONf_angle_d1.26111211
X-RAY DIFFRACTIONf_dihedral_angle_d17.3813013
X-RAY DIFFRACTIONf_chiral_restr0.0561245
X-RAY DIFFRACTIONf_plane_restr0.0071459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0971-2.12980.3191390.25182570X-RAY DIFFRACTION93
2.1298-2.16480.28621400.2362717X-RAY DIFFRACTION98
2.1648-2.20210.24551450.21712686X-RAY DIFFRACTION98
2.2021-2.24210.24071460.212709X-RAY DIFFRACTION99
2.2421-2.28520.27361490.21752721X-RAY DIFFRACTION98
2.2852-2.33190.30271410.21122733X-RAY DIFFRACTION99
2.3319-2.38260.25521490.20592730X-RAY DIFFRACTION98
2.3826-2.4380.23061310.19422722X-RAY DIFFRACTION99
2.438-2.4990.22191400.1942732X-RAY DIFFRACTION100
2.499-2.56650.27761310.1952772X-RAY DIFFRACTION99
2.5665-2.6420.27581310.1912743X-RAY DIFFRACTION99
2.642-2.72730.27311280.19892787X-RAY DIFFRACTION99
2.7273-2.82480.25521380.19182752X-RAY DIFFRACTION100
2.8248-2.93780.22511430.19742781X-RAY DIFFRACTION100
2.9378-3.07150.23341620.18532761X-RAY DIFFRACTION100
3.0715-3.23340.2431410.18552774X-RAY DIFFRACTION100
3.2334-3.43580.21391480.17752742X-RAY DIFFRACTION100
3.4358-3.7010.20331600.15772766X-RAY DIFFRACTION99
3.701-4.07310.17451280.1452775X-RAY DIFFRACTION99
4.0731-4.66180.1951450.13952794X-RAY DIFFRACTION100
4.6618-5.87070.18021640.16512788X-RAY DIFFRACTION100
5.8707-41.3550.17551280.15282856X-RAY DIFFRACTION99

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